Cover memmap parts with tests

Author: matteobachetti

hendrics/efsearch.py

@@ -517,6 +517,7 @@ def transient_search(
     t0=None,
     t1=None,
     oversample=4,
+    force_memmap=False,
 ):
     """Search for transient pulsations.
 
@@ -604,8 +605,8 @@ def transient_search(
         )
         if all_results is None:
             results_shape = (len(allvalues), nave.size, results.shape[1])
-            use_memmap = False
-            if np.prod(results_shape) > 1e7:
+            use_memmap = force_memmap
+            if np.prod(results_shape) > 1e7 or force_memmap:
                 import tempfile
 
                 tmp_results = tempfile.NamedTemporaryFile(delete=True).name + "_hen.npy"
@@ -902,6 +903,7 @@ def search_with_qffa(
     t0=None,
     t1=None,
     silent=False,
+    force_memmap=False,
 ):
     """'Quite fast folding' algorithm.
 
@@ -1008,7 +1010,7 @@ def local_show_progress(x):
             fgrid_shape = fgrid.shape
             all_fgrid_shape = (fgrid_shape[0] * len(allvalues), fgrid_shape[1])
             log.info(f"Initializing result arrays of shape {all_fgrid_shape}")
-            if all_fgrid_shape[0] * all_fgrid_shape[1] > 1e7:
+            if all_fgrid_shape[0] * all_fgrid_shape[1] > 1e7 or force_memmap:
                 import tempfile
 
                 log.info(
@@ -1710,6 +1712,12 @@ def _common_parser(args=None):
         help="The number of harmonics to use in the search "
         "(the 'N' in Z^2_N; only relevant to Z search!)",
     )
+    parser.add_argument(
+        "--force-memmap",
+        help="Force the use of memory-mapped files",
+        default=False,
+        action="store_true",
+    )
 
     args = check_negative_numbers_in_args(args)
     _add_default_args(parser, ["deorbit", "loglevel", "debug"])
@@ -1793,6 +1801,7 @@ def _common_main(args, func):
                 n=n,
                 nprof=args.n_transient_intervals,
                 oversample=oversample,
+                force_memmap=args.force_memmap,
             )
             plot_transient_search(results, out_fname + "_transient.gif")
             if not args.fast and not args.ffa:
@@ -1840,6 +1849,7 @@ def _common_main(args, func):
                 npfact=args.npfact,
                 oversample=oversample,
                 search_fdot=search_fdot,
+                force_memmap=args.force_memmap,
             )
 
             ref_time = (events.time[-1] + events.time[0]) / 2

hendrics/phaseogram.py

@@ -1039,37 +1039,36 @@ def main_phaseogram(args=None):
 
     log.setLevel(args.loglevel)
 
-    with log.log_to_file("HENphaseogram.log"):
-        if args.periodogram is None and args.freq is None:
-            raise ValueError("One of -f or --periodogram arguments MUST be " "specified")
-        elif args.periodogram is not None:
-            periodogram = load_folding(args.periodogram)
-            frequency = float(periodogram.peaks[0])
-            fdot = 0
-            fddot = 0
-        else:
-            frequency = args.freq
-            fdot = args.fdot
-            fddot = args.fddot
-
-        ip = run_interactive_phaseogram(
-            args.file,
-            freq=frequency,
-            fdot=fdot,
-            fddot=fddot,
-            nbin=args.nbin,
-            nt=args.ntimes,
-            test=args.test or args.get_toa,
-            binary=args.binary,
-            binary_parameters=args.binary_parameters,
-            pepoch=args.pepoch,
-            norm=args.norm,
-            plot_only=args.plot_only,
-            deorbit_par=args.deorbit_par,
-            emin=args.emin,
-            emax=args.emax,
-            colormap=args.colormap,
-        )
+    if args.periodogram is None and args.freq is None:
+        raise ValueError("One of -f or --periodogram arguments MUST be " "specified")
+    elif args.periodogram is not None:
+        periodogram = load_folding(args.periodogram)
+        frequency = float(periodogram.peaks[0])
+        fdot = 0
+        fddot = 0
+    else:
+        frequency = args.freq
+        fdot = args.fdot
+        fddot = args.fddot
+
+    ip = run_interactive_phaseogram(
+        args.file,
+        freq=frequency,
+        fdot=fdot,
+        fddot=fddot,
+        nbin=args.nbin,
+        nt=args.ntimes,
+        test=args.test or args.get_toa,
+        binary=args.binary,
+        binary_parameters=args.binary_parameters,
+        pepoch=args.pepoch,
+        norm=args.norm,
+        plot_only=args.plot_only,
+        deorbit_par=args.deorbit_par,
+        emin=args.emin,
+        emax=args.emax,
+        colormap=args.colormap,
+    )
     if args.get_toa:
         ip.toa(1)
 

hendrics/tests/test_efsearch.py

@@ -371,7 +371,8 @@ def test_zsearch_fdots(self):
         os.unlink(outfile)
 
     @pytest.mark.skipif("not HAS_IMAGEIO")
-    def test_transient(self):
+    @pytest.mark.parametrize("options", [["--force-memmap"], []])
+    def test_transient(self, options):
         evfile = self.dum
         main_zsearch(
             [
@@ -390,6 +391,7 @@ def test_transient(self):
                 "--n-transient-intervals",
                 "16",
             ]
+            + options
         )
         outfile = "events_Z22_9.85-9.95Hz_transient.gif"
         assert os.path.exists(outfile)
@@ -425,7 +427,8 @@ def test_zsearch_print_upperlim(self):
         # assert "Upper limit for sinusoids:" in caplog.text
         os.unlink(outfile)
 
-    def test_zsearch_fast(self):
+    @pytest.mark.parametrize("options", [["--force-memmap"], []])
+    def test_zsearch_fast(self, options):
         evfile = self.dum
         main_zsearch(
             [
@@ -441,6 +444,7 @@ def test_zsearch_fast(self):
                 "--oversample",
                 "4",
             ]
+            + options
         )
         outfile = "events_Z22_9.85-9.95Hz_fast" + HEN_FILE_EXTENSION
         assert os.path.exists(outfile)